knitr::opts_chunk$set(echo = TRUE, root.dir = here::here())
library(dplyr)
library(ggplot2)
set.seed(2019)bryois <- readxl::read_excel(here::here("data/metaanalysis/TableS2.xlsx"), sheet="Bryois2020_corr")
mat_bryois <- as.matrix(bryois$rg) %>% `rownames<-`(bryois$Trait2) %>% `colnames<-`("rg")
heat <- ggplot(bryois, aes(y=Trait2, x=1, fill=rg)) +
geom_tile() +
theme_bw()
plotly::ggplotly(heat)I began to explore this dataset but then realized it does not contain any Parkinson’s Disease GWAS.
rg = xlsx::read.xlsx(here::here("data/LD_Hub/LD-Hub_genetic_correlation_221x221_no_ENIGMA.xlsx"), sheetName = "rG") %>%
tibble::column_to_rownames("NA.")
colnames(rg) <- gsub("[.]","-",colnames(rg))
row.names(rg) <- gsub("[.]","-",row.names(rg))
rg[rg=="/"] <- NA
rg <- Matrix::as.matrix(rg, sparse = T)
rp = xlsx::read.xlsx(here::here("data/LD-Hub_genetic_correlation_221x221_no_ENIGMA.xlsx"), sheetName = "rP")%>%
tibble::column_to_rownames("NA.")
colnames(rp) <- gsub("[.]","-",colnames(rp))
row.names(rp) <- gsub("[.]","-",row.names(rp))
rp[rp=="/"] <- NA
rp <- Matrix::as.matrix(rp, sparse = T)Check for Parkinson’s
grep("Parkinson",colnames(rp), ignore.case = T, value = T)utils::sessionInfo()## R version 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggplot2_3.3.5 dplyr_1.0.7
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.7 cellranger_1.1.0 pillar_1.6.2 bslib_0.2.5.1
## [5] compiler_4.1.0 jquerylib_0.1.4 tools_4.1.0 digest_0.6.27
## [9] viridisLite_0.4.0 jsonlite_1.7.2 evaluate_0.14 lifecycle_1.0.0
## [13] tibble_3.1.3 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.11
## [17] DBI_1.1.1 crosstalk_1.1.1 yaml_2.2.1 xfun_0.25
## [21] httr_1.4.2 withr_2.4.2 stringr_1.4.0 knitr_1.33
## [25] htmlwidgets_1.5.3 generics_0.1.0 vctrs_0.3.8 sass_0.4.0
## [29] rprojroot_2.0.2 grid_4.1.0 tidyselect_1.1.1 data.table_1.14.0
## [33] glue_1.4.2 here_1.0.1 R6_2.5.0 plotly_4.9.4.9000
## [37] fansi_0.5.0 readxl_1.3.1 rmarkdown_2.10 farver_2.1.0
## [41] tidyr_1.1.3 purrr_0.3.4 magrittr_2.0.1 scales_1.1.1
## [45] ellipsis_0.3.2 htmltools_0.5.1.1 assertthat_0.2.1 colorspace_2.0-2
## [49] labeling_0.4.2 utf8_1.2.2 stringi_1.7.3 lazyeval_0.2.2
## [53] munsell_0.5.0 crayon_1.4.1